Gigs it sounds like the same issue I was having or very close. I deleted all of my server files except for the config file , new world folder and my scripts folder. I downloaded a fresh copy of the server from the site and it seems to have solved the endpoint errors I was having. When I did my updates in the past I would drag and drop and overwrite as necessary. Looks like the way for me to do it will be delete and re insert the server files.
When i do a update i do it all new and fresh into a new folder with the date of the day i did it then all i copy to that folder is the world file the settings file and the script folder so all other files are new maybe they have a more updated server ill re download that and see anyway
Cheers